The number of RILs is 4,027 and the number of markers is 71,196. Mixed linear model based association analysis.
.mlma (columns are chromosome, Markers, physical position, reference allele (the coded effect allele), the other allele, frequency of the reference allele, SNP effect, standard error and p-value).
The significant QTLs are defined by -log10(p-value) > FDR (0.05).
library("IHW")
get_bh_threshold(GWAS.Results$p[!is.na(GWAS.Results$p)], 0.05)
For a few of traits, FDR threshold is not there, 5 is used.
36 output files are for 36 traits, each having 10 chromosomes.
The number of RILs is 4,027 and the number of markers is 20,470,711.
Mixed linear model based association analysis.
.mlma (columns are chromosome, Markers, physical position, reference allele (the coded effect allele),
the other allele, frequency of the reference allele, SNP effect, standard error and p-value).
The significant QTLs are defined by -log10(p-value) > FDR (0.05).
library("IHW")
get_bh_threshold(GWAS.Results$p[!is.na(GWAS.Results$p)], 0.05)
For a few of traits, FDR threshold is not there, 5 is used.
360 output files are combinations of 36 traits and 10 chromosomes.